HEADER PROTEIN FIBRIL 28-JAN-14 4ONK TITLE [LEU-5]-ENKEPHALIN MUTANT - YVVFL COMPND MOL_ID: 1; COMPND 2 MOLECULE: [LEU-5]-ENKEPHALIN MUTANT - YVVFL; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 OTHER_DETAILS: SYNTHESIZED KEYWDS AMYLOID-LIKE PROTOFIBRIL, PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR S.SANGWAN,D.EISENBERG,M.R.SAWAYA,T.D.DO,M.T.BOWERS,N.E.LAPOINTE, AUTHOR 2 D.B.TEPLOW,S.C.FEINSTEIN REVDAT 4 03-APR-24 4ONK 1 REMARK REVDAT 3 28-FEB-24 4ONK 1 REMARK REVDAT 2 06-AUG-14 4ONK 1 JRNL REVDAT 1 02-JUL-14 4ONK 0 JRNL AUTH T.D.DO,N.E.LAPOINTE,S.SANGWAN,D.B.TEPLOW,S.C.FEINSTEIN, JRNL AUTH 2 M.R.SAWAYA,D.S.EISENBERG,M.T.BOWERS JRNL TITL FACTORS THAT DRIVE PEPTIDE ASSEMBLY FROM NATIVE TO AMYLOID JRNL TITL 2 STRUCTURES: EXPERIMENTAL AND THEORETICAL ANALYSIS OF JRNL TITL 3 [LEU-5]-ENKEPHALIN MUTANTS. JRNL REF J.PHYS.CHEM.B V. 118 7247 2014 JRNL REFN ISSN 1089-5647 JRNL PMID 24915112 JRNL DOI 10.1021/JP502473S REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_1457 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : LS_WUNIT_K1 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 9.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 35.130 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 522 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.000 REMARK 3 FREE R VALUE TEST SET COUNT : 47 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 0.0000 - 1.9003 0.94 475 47 0.1513 0.1994 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.660 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.11 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 94 REMARK 3 ANGLE : 0.842 128 REMARK 3 CHIRALITY : 0.039 16 REMARK 3 PLANARITY : 0.006 14 REMARK 3 DIHEDRAL : 10.952 28 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4ONK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-FEB-14. REMARK 100 THE DEPOSITION ID IS D_1000084717. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-AUG-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 3 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 537 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.15100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.15300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.2 REMARK 200 STARTING MODEL: IDEAL BETA STRAND WITH SEQUENCE AVVAA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVOIR CONTAINED 25% PEG 3350, 0.2M REMARK 280 POTASSIUM THIOCYANATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE BIOLOGICAL UNIT IS A PAIR OF BETA SHEETS. ONE SHEET IS REMARK 300 CONSTRUCTED FROM CHAINS A AND B WITH UNIT CELL TRANSLATIONS ALONG REMARK 300 THE A DIRECTION (I.E. X+1,Y,Z; X+2,Y,Z; X+3,Y,Z, ETC.). THE SECOND REMARK 300 SHEET IS CONSTRUCTED FROM X,Y+1,Z; X+1,Y+1,Z; X+2,Y+1,Z; ETC.). REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DODECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 9.61300 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 19.22600 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 -4.34157 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 13.12771 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 5.27143 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 13.12771 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 6 1.000000 0.000000 0.000000 14.88443 REMARK 350 BIOMT2 6 0.000000 1.000000 0.000000 13.12771 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 0.00000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4OLR RELATED DB: PDB REMARK 900 LEU-5 ENKEPHALIN MUTANT DBREF 4ONK A 1 5 PDB 4ONK 4ONK 1 5 DBREF 4ONK B 1 5 PDB 4ONK 4ONK 1 5 SEQRES 1 A 5 TYR VAL VAL PHE LEU SEQRES 1 B 5 TYR VAL VAL PHE LEU FORMUL 3 HOH *3(H2 O) SHEET 1 A 2 VAL A 2 PHE A 4 0 SHEET 2 A 2 VAL B 2 PHE B 4 -1 O PHE B 4 N VAL A 2 CRYST1 9.613 13.827 14.835 90.61 103.12 108.30 P 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.104026 0.034397 0.027390 0.00000 SCALE2 0.000000 0.076173 0.006768 0.00000 SCALE3 0.000000 0.000000 0.069486 0.00000 ATOM 1 N TYR A 1 1.565 0.138 -1.868 1.00 15.08 N ATOM 2 CA TYR A 1 1.230 0.193 -0.445 1.00 15.38 C ATOM 3 C TYR A 1 1.824 1.417 0.229 1.00 14.41 C ATOM 4 O TYR A 1 3.029 1.629 0.160 1.00 11.24 O ATOM 5 CB TYR A 1 1.726 -1.060 0.266 1.00 13.95 C ATOM 6 CG TYR A 1 1.461 -1.082 1.756 1.00 13.59 C ATOM 7 CD1 TYR A 1 0.226 -1.478 2.249 1.00 16.41 C ATOM 8 CD2 TYR A 1 2.452 -0.732 2.670 1.00 13.76 C ATOM 9 CE1 TYR A 1 -0.027 -1.515 3.603 1.00 16.02 C ATOM 10 CE2 TYR A 1 2.208 -0.758 4.035 1.00 15.36 C ATOM 11 CZ TYR A 1 0.966 -1.156 4.492 1.00 19.20 C ATOM 12 OH TYR A 1 0.702 -1.200 5.840 1.00 21.18 O ATOM 13 N VAL A 2 0.987 2.225 0.879 1.00 10.79 N ATOM 14 CA VAL A 2 1.489 3.393 1.604 1.00 12.56 C ATOM 15 C VAL A 2 0.795 3.578 2.944 1.00 12.02 C ATOM 16 O VAL A 2 -0.429 3.462 3.043 1.00 10.79 O ATOM 17 CB VAL A 2 1.312 4.695 0.799 1.00 14.29 C ATOM 18 CG1 VAL A 2 1.815 5.888 1.598 1.00 12.86 C ATOM 19 CG2 VAL A 2 2.018 4.619 -0.544 1.00 16.40 C ATOM 20 N VAL A 3 1.578 3.862 3.978 1.00 9.30 N ATOM 21 CA VAL A 3 1.013 4.295 5.249 1.00 11.13 C ATOM 22 C VAL A 3 1.669 5.604 5.670 1.00 11.64 C ATOM 23 O VAL A 3 2.895 5.717 5.662 1.00 10.32 O ATOM 24 CB VAL A 3 1.195 3.225 6.352 1.00 8.88 C ATOM 25 CG1 VAL A 3 0.769 3.762 7.704 1.00 11.59 C ATOM 26 CG2 VAL A 3 0.399 1.989 6.013 1.00 11.53 C ATOM 27 N PHE A 4 0.856 6.604 6.002 1.00 9.31 N ATOM 28 CA PHE A 4 1.381 7.825 6.601 1.00 11.61 C ATOM 29 C PHE A 4 0.805 8.011 7.998 1.00 13.96 C ATOM 30 O PHE A 4 -0.411 7.936 8.190 1.00 11.95 O ATOM 31 CB PHE A 4 1.073 9.057 5.745 1.00 11.36 C ATOM 32 CG PHE A 4 1.344 10.352 6.454 1.00 13.26 C ATOM 33 CD1 PHE A 4 2.640 10.834 6.565 1.00 12.66 C ATOM 34 CD2 PHE A 4 0.313 11.070 7.044 1.00 14.79 C ATOM 35 CE1 PHE A 4 2.907 12.013 7.243 1.00 14.35 C ATOM 36 CE2 PHE A 4 0.569 12.251 7.725 1.00 15.02 C ATOM 37 CZ PHE A 4 1.872 12.725 7.825 1.00 16.54 C ATOM 38 N LEU A 5 1.676 8.257 8.970 1.00 11.16 N ATOM 39 CA LEU A 5 1.224 8.495 10.336 1.00 13.03 C ATOM 40 C LEU A 5 1.867 9.743 10.943 1.00 16.38 C ATOM 41 O LEU A 5 3.085 9.920 10.904 1.00 13.52 O ATOM 42 CB LEU A 5 1.520 7.283 11.214 1.00 15.47 C ATOM 43 CG LEU A 5 0.895 7.373 12.605 1.00 18.47 C ATOM 44 CD1 LEU A 5 -0.552 7.755 12.467 1.00 20.64 C ATOM 45 CD2 LEU A 5 0.986 6.058 13.319 1.00 22.76 C ATOM 46 OXT LEU A 5 1.182 10.603 11.508 1.00 15.56 O TER 47 LEU A 5 ATOM 48 N TYR B 1 -3.954 10.206 9.758 1.00 12.93 N ATOM 49 CA TYR B 1 -3.486 8.872 9.383 1.00 14.65 C ATOM 50 C TYR B 1 -4.150 8.387 8.107 1.00 13.84 C ATOM 51 O TYR B 1 -5.365 8.453 7.983 1.00 13.58 O ATOM 52 CB TYR B 1 -3.764 7.875 10.507 1.00 11.56 C ATOM 53 CG TYR B 1 -3.535 6.427 10.134 1.00 14.66 C ATOM 54 CD1 TYR B 1 -2.303 5.831 10.340 1.00 13.98 C ATOM 55 CD2 TYR B 1 -4.560 5.645 9.599 1.00 14.45 C ATOM 56 CE1 TYR B 1 -2.085 4.502 10.025 1.00 17.66 C ATOM 57 CE2 TYR B 1 -4.349 4.309 9.272 1.00 17.46 C ATOM 58 CZ TYR B 1 -3.103 3.744 9.490 1.00 17.32 C ATOM 59 OH TYR B 1 -2.866 2.423 9.178 1.00 18.48 O ATOM 60 N VAL B 2 -3.365 7.874 7.167 1.00 11.39 N ATOM 61 CA VAL B 2 -3.955 7.245 6.002 1.00 10.32 C ATOM 62 C VAL B 2 -3.200 5.980 5.643 1.00 11.60 C ATOM 63 O VAL B 2 -1.976 5.900 5.779 1.00 8.29 O ATOM 64 CB VAL B 2 -3.992 8.195 4.776 1.00 12.92 C ATOM 65 CG1 VAL B 2 -2.587 8.472 4.254 1.00 12.80 C ATOM 66 CG2 VAL B 2 -4.866 7.608 3.665 1.00 11.13 C ATOM 67 N VAL B 3 -3.949 4.978 5.207 1.00 10.85 N ATOM 68 CA VAL B 3 -3.351 3.805 4.600 1.00 11.67 C ATOM 69 C VAL B 3 -4.038 3.567 3.267 1.00 11.22 C ATOM 70 O VAL B 3 -5.263 3.625 3.167 1.00 9.02 O ATOM 71 CB VAL B 3 -3.467 2.555 5.505 1.00 11.70 C ATOM 72 CG1 VAL B 3 -4.896 2.366 5.994 1.00 11.87 C ATOM 73 CG2 VAL B 3 -2.975 1.315 4.770 1.00 12.95 C ATOM 74 N PHE B 4 -3.255 3.346 2.223 1.00 12.24 N ATOM 75 CA PHE B 4 -3.870 2.925 0.982 1.00 12.78 C ATOM 76 C PHE B 4 -3.057 1.864 0.274 1.00 14.83 C ATOM 77 O PHE B 4 -1.828 1.850 0.334 1.00 12.15 O ATOM 78 CB PHE B 4 -4.133 4.116 0.061 1.00 15.64 C ATOM 79 CG PHE B 4 -2.951 5.007 -0.188 1.00 16.11 C ATOM 80 CD1 PHE B 4 -2.647 6.045 0.685 1.00 20.56 C ATOM 81 CD2 PHE B 4 -2.201 4.873 -1.345 1.00 17.43 C ATOM 82 CE1 PHE B 4 -1.579 6.908 0.433 1.00 18.84 C ATOM 83 CE2 PHE B 4 -1.138 5.728 -1.604 1.00 18.61 C ATOM 84 CZ PHE B 4 -0.833 6.752 -0.715 1.00 18.54 C ATOM 85 N LEU B 5 -3.765 0.954 -0.380 1.00 14.34 N ATOM 86 CA LEU B 5 -3.119 -0.197 -0.977 1.00 12.93 C ATOM 87 C LEU B 5 -3.948 -0.759 -2.118 1.00 14.20 C ATOM 88 O LEU B 5 -5.173 -0.691 -2.085 1.00 13.42 O ATOM 89 CB LEU B 5 -2.879 -1.263 0.092 1.00 15.25 C ATOM 90 CG LEU B 5 -4.081 -1.683 0.947 1.00 15.53 C ATOM 91 CD1 LEU B 5 -4.844 -2.842 0.324 1.00 16.23 C ATOM 92 CD2 LEU B 5 -3.624 -2.051 2.342 1.00 15.90 C ATOM 93 OXT LEU B 5 -3.418 -1.303 -3.086 1.00 14.69 O TER 94 LEU B 5 HETATM 95 O HOH A 101 -2.482 12.660 8.666 1.00 18.12 O HETATM 96 O HOH B 101 0.109 2.087 -2.898 1.00 22.25 O HETATM 97 O HOH B 102 -3.592 2.493 -4.306 1.00 13.75 O MASTER 199 0 0 0 2 0 0 6 95 2 0 2 END